#include <corelib/ncbistl.hpp>
#include <string>
#include <list>
#include <iostream>
#include <algo/align/prosplign/prosplign.hpp>
Go to the source code of this file.
Go to the SVN repository for this file.
list< CNPiece > FindGoodParts (const CProteinAlignText &alignment_text, CProSplignOutputOptionsExt options, const CProSplignScaledScoring &scoring, const CSubstMatrix &matrix) list< CNPiece > ExcludeBadExons (const CNPiece pc, const string &match_all_pos, const string &protein, CProSplignOutputOptionsExt m_options) list< CNPiece > FindGoodParts (const CNPiece pc, const string &match_all_pos, const string &protein, CProSplignOutputOptionsExt m_options) bool TrimNegativeTail (CNPiece &pc, const CProteinAlignText &alignment_text, const CProSplignScaledScoring &scoring, const CSubstMatrix &matrix) void RefineAlignment (objects::CScope &scope, objects::CSeq_align &seq_align, const list< CNPiece > &good_parts) void SetScores (objects::CSeq_align &seq_align, objects::CScope &scope, const string &matrix_name="BLOSUM62") ◆ ExcludeBadExons()Definition at line 388 of file Info.cpp.
References CNPiece::beg, CNPiece::end, CProSplignOutputOptions::GetMinExonId(), CProSplignOutputOptions::GetMinExonPos(), i, INTRON_CHAR, len, match(), MATCH_CHAR, n, and POSIT_CHAR.
Referenced by FindGoodParts().
◆ FindGoodParts() [1/2]Definition at line 273 of file Info.cpp.
References CProSplignOutputOptionsExt::BackCheck(), CProSplignOutputOptionsExt::Bad(), BAD_OR_MISMATCH, CNPiece::beg, CProSplignOutputOptionsExt::Dropof(), CNPiece::end, CProSplignOutputOptionsExt::ForwCheck(), GAP_CHAR, CProSplignOutputOptions::GetMinGoodLen(), CProSplignOutputOptions::GetStartBonus(), INTRON_CHAR, CProSplignOutputOptionsExt::Join(), match(), MATCH_CHAR, n, CProSplignOutputOptionsExt::Perc(), POSIT_CHAR, and CProSplignOutputOptionsExt::splice_cost.
◆ FindGoodParts() [2/2]Definition at line 107 of file Info.cpp.
References _ASSERT, CNPiece::beg, CProSplignTrimmer::CutFromLeft(), CProSplignTrimmer::CutFromRight(), CNPiece::end, ExcludeBadExons(), FindGoodParts(), GAP_CHAR, CProSplignOutputOptions::GetCutFlankPartialCodons(), CProSplignOutputOptions::GetCutNs(), CProteinAlignText::GetDNA(), CProSplignOutputOptions::GetFillHoles(), CProteinAlignText::GetMatch(), CProSplignOutputOptions::GetMinHoleLen(), CProteinAlignText::GetProtein(), i, INTRON_CHAR, islower(), CProSplignOutputOptions::IsPassThrough(), isupper(), match(), MATCH_CHAR, n, nuc, POSIT_CHAR, CProSplignTrimmer::RestoreFivePrime(), CProSplignTrimmer::RestoreThreePrime(), SPACE_CHAR, tmp, and TrimNegativeTail().
Referenced by FindGoodParts(), and CProSplign::RefineAlignment().
◆ RefineAlignment() ◆ SetScores() ◆ TrimNegativeTail()Definition at line 438 of file Info.cpp.
References CNPiece::beg, CNPiece::end, GAP_CHAR, CProteinAlignText::GetDNA(), CProteinAlignText::GetProtein(), CProteinAlignText::GetTranslation(), INTRON_CHAR, islower(), isupper(), n, NCBI_THROW, nuc, prot, CSubstMatrix::ScaledScore(), CProSplignScaledScoring::sm_Ig, CProSplignScaledScoring::sm_Ine, and toupper().
Referenced by FindGoodParts().
RetroSearch is an open source project built by @garambo | Open a GitHub Issue
Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo
HTML:
3.2
| Encoding:
UTF-8
| Version:
0.7.4